I don't know the exact wording of her statement, so this may be completly rubbish, but please bear with me.
We all assume she meant BO2 wasn't because of SR2, right? Well, what if by "altered timeline" she meant the one Mobeius created. Mobeius controlled and manipulated to try and get Raziel into the Reaver, but what if she meant not that route, but the original route, the "true destiny" route?

